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PubMed1999

Purification, identification, and cDNA cloning of Cha o 2, the second major allergen of Japanese cypress pollen.

The second major allergen of Chamaecyparis obtusa (Japanese cypress) pollen, Cha o 2, has been purified and its cDNA cloned. Of patients with pollinosis caused by C. obtusa, 82.5% produce IgE antibodies which react with purified Cha o 2. The purified protein has a molecular mass of 46 kDa and its 12 N-terminal amino acid sequence displays a high homology with that of Cry j 2, the second major allergen of Cryptomeria japonica pollen. cDNA clones coding for Cha o 2 have been isolated using Cry j 2 cDNA as a probe. Cha o 2 cDNA clones were sequenced and found to code a putative 50-residue signal sequence and a 464-residue mature protein with a molecular weight of 50 kDa. Two possible N-linked glycosylation sites were found in the sequence. The deduced amino acid sequence of Cha o 2 shows 74.3% identity with that of Cry j 2. In its primary structure, Cha o 2 shows significant identity with those of the polygalacturonases of avocado, tomato, and maize as well as Cry j 2.

Allergens↗

PubMed2001

Three-dimensional structure of Erwinia chrysanthemi pectin methylesterase reveals a novel esterase active site.

Most structures of neutral lipases and esterases have been found to adopt the common alpha/beta hydrolase fold and contain a catalytic Ser-His-Asp triad. Some variation occurs in both the overall protein fold and in the location of the catalytic triad, and in some enzymes the role of the aspartate residue is replaced by a main-chain carbonyl oxygen atom. Here, we report the crystal structure of pectin methylesterase that has neither the common alpha/beta hydrolase fold nor the common catalytic triad. The structure of the Erwinia chrysanthemi enzyme was solved by multiple isomorphous replacement and refined at 2.4 A to a conventional crystallographic R-factor of 17.9 % (R(free) 21.1 %). This is the first structure of a pectin methylesterase and reveals the enzyme to comprise a right-handed parallel beta-helix as seen in the pectinolytic enzymes pectate lyase, pectin lyase, polygalacturonase and rhamnogalacturonase, and unlike the alpha/beta hydrolase fold of rhamnogalacturonan acetylesterase with which it shares esterase activity. Pectin methylesterase has no significant sequence similarity with any protein of known structure. Sequence conservation among the pectin methylesterases has been mapped onto the structure and reveals that the active site comprises two aspartate residues and an arginine residue. These proposed catalytic residues, located on the solvent-accessible surface of the parallel beta-helix and in a cleft formed by external loops, are at a location similar to that of the active site and substrate-binding cleft of pectate lyase. The structure of pectin methylesterase is an example of a new family of esterases.

Amino Acid Sequence↗

PubMed1992

Molecular biology of fruit ripening and its manipulation with antisense genes.

Considerable progress in tomato molecular biology has been made over the past five years. At least 19 different mRNAs which increase in amount during tomato fruit ripening have been cloned and genes for enzymes involved in cell wall degradation (polygalacturonase and pectinesterase) and ethylene synthesis (ACC synthase) have been identified by conventional procedures. Transgenic plants have been used to identify regions of DNA flanking fruit-specific, ripening-related and ethylene-regulated genes and trans-acting factors which bind to these promoters have also been identified. Antisense genes expressed in transgenic plants have proved to be highly effective for inhibiting the specific expression of ripening-related genes. These experiments have changed our understanding of how softening occurs in tomato fruit. Antisense techniques have also been used to identify genes encoding enzymes for carotenoid biosynthesis (phytoene synthase) and ethylene biosynthesis (the ethylene-forming enzyme). The altered characteristics of fruit transformed with specific antisense genes, such as retarded ripening and resistance to splitting, may prove to be of value to fruit growers, processors and ultimately the consumer.

Antisense Elements (Genetics)↗

PubMed1989

Isolation and characterization of a fruit-specific cDNA and the corresponding genomic clone from tomato.

Differential screening of a cDNA bank constructed from ripe tomato fruit mRNA allowed the isolation of cDNA clone 2A11 which is entirely fruit-specific, is expressed at steadily increasing levels from anthesis to breaker, and accounts for approximately 1% of the messenger RNA in mature tomato fruit. A genomic clone corresponding to the 2A11 cDNA was isolated from a tomato genomic library. Sequence comparison of the cDNA clone with the genomic clone shows they are identical over the shared region with the genomic clone possessing a single large intron near the 5' end of the message. The open reading frame of 2A11 would encode a sulfur-rich polypeptide 96 amino acids in length. The identity of the putative protein is unknown. In situ hybridization shows that the 2A11 message is found throughout the pericarp cells in a tomato fruit. In contrast, in situ hybridization of early ripening stages with a polygalacturonase probe shows higher mRNA levels in cells of the outer pericarp and cells surrounding the vascular regions of the pericarp.

Amino Acid Sequence↗

PubMed2002

Production of gamma-linolenic acid by Cunninghamella echinulata cultivated on glucose and orange peel.

A newly isolated strain of Cunninghamella echinulata grown on glucose produced significant quantities of biomass and cellular lipids in media with high C/N ratio. The oil yield from glucose consumed increased after nitrogen exhaustion in the growth medium, but gamma-linolenic acid (GLA) content in cellular oil systematically decreased during the lipid accumulation process. When lipid accumulation was completed, GLA concentration in the cellular lipids progressively increased. The highest GLA production (720 mg/l) was achieved in medium with a C/N ratio equal to 163. C. echinulata was also able to grow on orange peel. The C/N ratio in the orange peel decreased from 50 to 26 during solid-state fermentation. Maximum oxygen uptake was observed during assimilation of reducing sugars, whereas a polygalacturonase activity was detected after reducing sugars had been exhausted. The maximum GLA production was 1.2-1.5 mg/g of fermented peel, calculated on a dry weight basis. After enrichment of the pulp with inorganic nitrogen and glucose, an increase in the production of oil and GLA was observed.

Bioreactors↗

PubMed2002

Altered cell wall disassembly during ripening of Cnr tomato fruit: implications for cell adhesion and fruit softening.

The Cnr ( C olourless n on- r ipening) tomato ( Lycopersicon esculentum Mill.) mutant has an aberrant fruit-ripening phenotype in which fruit do not soften and have reduced cell adhesion between pericarp cells. Cell walls from Cnr fruit were analysed in order to assess the possible contribution of pectic polysaccharides to the non-softening and altered cell adhesion phenotype. Cell wall material (CWM) and solubilised fractions of mature green and red ripe fruit were analysed by chemical, enzymatic and immunochemical techniques. No major differences in CWM sugar composition were detected although differences were found in the solubility and composition of the pectic polysaccharides extracted from the CWM at both stages of development. In comparison with the wild type, the ripening-associated solubilisation of homogalacturonan-rich pectic polysaccharides was reduced in Cnr. The proportion of carbohydrate that was chelator-soluble was 50% less in Cnr cell walls at both the mature green and red ripe stages. Chelator-soluble material from ripe-stage Cnr was more susceptible to endo-polygalacturonase degradation than the corresponding material from wild-type fruit. In addition, cell walls from Cnr fruit contained larger amounts of galactosyl- and arabinosyl-containing polysaccharides that were tightly bound in the cell wall and could only be extracted with 4 M KOH, or remained in the insoluble residue. The complexity of the cell wall alterations that occur during fruit ripening and the significance of different extractable polymer pools from cell walls are discussed in relation to the Cnr phenotype.

Cell Adhesion↗

PubMed2026

Seed shattering habit in millets and the secrets of the abscission layer - a comprehensive review.

Though seed shattering continues to be a significant barrier affecting yield stability and harvesting efficiency in millets and other grasses, millets are increasingly acknowledged as climate-resilient, nutrient-rich 2007cereal crops with the potential to strengthen global nutritional and food security under the combined pressures of climate change, population growth, and limited natural resources. Since strong artificial selection favoured non-shattering phenotypes during domestication, seed shattering, an adaptive trait in wild species that promotes seed dispersal through the formation and activation of specialised abscission layers, became a distinguishing feature of cultivated cereals. With a focus on the morphological, physiological, hormonal, and genetic modulation of the abscission zone, this article summarizes the state of the art regarding seed shattering in millets. Abscission layer morphology, location, and lignification vary greatly among grasses, from well-defined lignified zones in rice and sorghum to non-lignified and anatomically subtle zones in Setaria and Panicum species. Cell wall-modifying enzymes like polygalacturonases, cellulases, expansins, and pectin methylesterases that mediate middle lamella degradation are modulated by coordinated hormonal signalling involving auxin, ethylene, and abscisic acid, which controls the timing and progression of cell separation at the physiological level. Domestication-related genes, including SH1, qSH1, SH4, and LES1, demonstrate convergent evolutionary mechanisms controlling abscission layer development in a variety of grass lineages at the molecular level. Understanding these regulatory networks has been greatly enhanced by recent developments in transcriptomics, functional genomics, and genome sequencing in both model species and underused millets. The role of millets as climate-smart cereals for sustainable future agriculture is reinforced by the integration of anatomical, physiological, and genetic insights, which offer a solid basis for targeted breeding and genome-editing strategies intended to improve seed retention, enhance yield stability, and increase harvest efficiency.

Abscission Layer↗

PubMed2026

Scalable production of pectinases from Bacillus licheniformis SMIA-2 using agro-Industrial by-products with genomic insights.

UNLABELLED: The study re-analyzed the draft genome of Bacillus licheniformis SMIA-2 and generated a reference-guided pseudo-scaffold. Cross-validated genome annotation identified five candidate loci associated with pectin degradation, including putative pectate lyases, polygalacturonase, and downstream uronate-catabolic genes. Submerged fermentation with passion fruit peel flour and corn steep liquor yielded crude enzymatic extracts, which were spray-dried at 110 °C using maltodextrin and microcrystalline cellulose as stabilizers. The dried formulation retained pectinase activity for 180 days at 5 °C and showed additional cellulase, amylase, xylanase, and protease activities. Pectinase displayed optimal activity at pH 8.5 and 70 °C, with stability between pH 8.0-8.5 and 65-70 °C. Despite not using a reference strain and the absence of some omics analyses, with genomic and industrial claims presented as evidence of biotechnological potential rather than definitive functional validation of individual genes, these results support a sustainable, scalable, and alkaline-tolerant enzyme platform based on agro-industrial residues. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at https://doi.org/10.1007/s10068-026-02252-3.

Agro-industrial residues↗

PubMed2005

New effective method for analysis of the component composition of enzyme complexes from Trichoderma reesei.

A method for analysis of the component composition of multienzyme complexes secreted by the filamentous fungus Trichoderma reesei was developed. The method is based on chromatofocusing followed by further identification of protein fractions according to their substrate specificity and molecular characteristics of the proteins. The method allows identifying practically all known cellulases and hemicellulases of T. reesei: endoglucanase I (EG I), EG II, EG III, cellobiohydrolase I (CBH I), CBH II, xylanase I (XYL I), XYL II, beta-xylosidase, alpha-L-arabinofuranosidase, acetyl xylan esterase, mannanase, alpha-galactosidase, xyloglucanase, polygalacturonase, and exo-beta-1,3-glucosidase. The component composition of several laboratory and commercial T. reesei preparations was studied and the content of the individual enzymes in these preparations was quantified. The influence of fermentation conditions on the component composition of secreted enzyme complexes was revealed. The characteristic features of enzyme preparations obtained in "cellulase" and "xylanase" fermentation conditions are shown.

Binding Sites↗

PubMed2004

Pectic zymogram variation and pathogenicity of Rhizoctonia solani AG-4 to bean (Phaseolus vulgaris) isolates in Isfahn, Iran.

Rhizoctonia disease, caused by Rhizoctonia solani is one of the most important fungal diseases in bean fields in Isfahan, Iran. Bean plants showing stem and root cankers were collected and Rhizoctonia-like fungi obtained from the samples were identified by anastomosis. Pure cultures of bean isolates of R. solani were identified as AG-4. There were also AG-4 isolates from tomato, potato, cucumber, alfalfa and sugar beet in the areas sampled. A total of 163 isolates of R. solani AG-4 originating from stem and root cankers of beans were examined using pectic zymogram electrophoresis. Polygalacturonase (PG) and pectin estrase isozymes were observed in all AG-4 isolates tested. One (PG) and one pectic esterase (PE) band was found in common between all isolates examined. The electrophoretic patterns were grouped into seven zymogram groups (ZGs) according to the diagnostic PG and PE bands. One ZG occurred in a high frequency throughout the areas sampled. A pathogenicity test was conducted and representative isolates of each ZG were used to inoculate healthy bean plants. The results showed that each ZG caused different symptoms with varying severity. Isolates belonging to two ZGs were highly pathogenic causing root, stem and hypocotyl cankers whereas isolates of the other ZGs produced weak or no symptoms.

Electrophoresis, Agar Gel↗

PubMed1976

Characterization of two endopolygalacturonase isozymes produced by Fusarium oxysporum f. sp. lycopersici.

Polygalacturonase (EC 3.2.1.15) produced by Fursarium oxysporum f. sp. lycopersici was purified by chromatography on DEAE-cellulose, CM-cellulose, and hydroxyapatite. The purified enzyme consisted of two electrophoretically distinct "isozymes", that behaved as charge isomers during electrophoresis in several different concentrations of polyacrylamide gel. The two isozymes had similar "endo" modes of action on polygalacturonic acid, as determined by comparison of viscosity reduction, reducing group release, and thin-layer chromatography of oligomeric hydrolysis products. Both isozymes hydrolzyed 5% of the substrate bonds in reaching 50% viscosity reduction. The amino acid compositions of the isozymes were similar and their molecular weights were about 37000 as determined by sedimentation equilibrium. Removal of large amounts of carbohydrate during purification did not affect heat stability of the enzymes. A large proportion of the remaining carbohydrate appeared to be covalently linked to the enzyme protein.

Amino Acids↗

PubMed1989

Structural characterization of an anti-complementary pectic polysaccharide from the roots of Bupleurum falcatum L.

An anti-complementary pectic polysaccharide (BR-2-IIb), isolated from the roots of Bupleurum falcatum L., has an average molecular weight of 36,000 (gel filtration), and was subjected to methylation analysis before and after carboxyl-reduction, digestion with endo-polygalacturonase, base-catalysed beta-elimination, and partial acid hydrolysis. BR-2-IIb consisted mainly of galacturonic acid, arabinose, rhamnose, and galactose in the molar ratios 13.0:2.1:1.4:1.0 and contained a large enzyme-sensitive polygalacturonan region. The enzyme-resistant region (PG-1) was rich in neutral sugars and contained a backbone of 4-linked GalA and 2-linked Rha to which a highly branched arabinogalactan was attached to position 4 of some 2-linked Rha units. Partial acid hydrolysis of BR-2-IIb gave Ara-(1----3)-Ara, Ara-(1----4)-Arap, Ara-(1----5)-Araf, Ara-(1----6)-Gal, Gal-(1----4)-Gal, GalA-(1----2)-Rha, GalA-(1----4)-Rha, GalA----Rha----Rha, Gal----Rha----Rha, and GlA-(1----6)-Gal in addition to (1----4)linked oligogalacturonides. The anticomplementary activity of BR-2-IIb was enhanced by de-esterification, but carboxyl-reduction decreased the activity.

Carbohydrate Sequence↗

PubMed1989

Relationship between structure and activity of the "ramified" region in anti-complementary pectic polysaccharides from Angelica acutiloba Kitagawa.

One of the anti-complementary pectic polysaccharides (AR-2IIa) isolated from the root of Angelica acutiloba Kitagawa gives the "ramified" region (PG-1a,rhamnogalacturonan with neutral side-chains) in addition to oligogalacturonides on digestion with endo-alpha-D-(1--4)-polygalacturonase. When the neutral side-chains in PG-1a were digested with both exo-alpha-L-arabinofuranosidase and exo-beta-D-galactosidase, approximately 70% of the arabinosyl chains and approximately 30% of the galactosyl chains were released. The resistant product E-PG-1a had the same anti-complementary activity as PG-1a. E-PG-1a gave long (d.p. greater than or equal to 5) and short (d.p. less than or equal to 4) neutral galactosyl chains after degradation of the GalA moiety by base-catalysed beta-elimination in the presence of sodium borodeuteride followed with lithium-mediated degradation. Methylation analysis showed that the long galactosyl chains consisted mainly of terminal, 6-linked and 3,6-disubstituted Gal, and that the short chains were rich in 6-linked Gal. Degradation of the GalA moieties in PG-1a markedly decreased the anti-complementary activity, but the long and short galactosyl chains still expressed approximately 50 and approximately 20%, respectively, of the anti-complementary activity of E-PG-1a.

Animals↗

PubMed1991

Partial structure of an anti-ulcer pectic polysaccharide from the roots of Bupleurum falcatum L.

Methylation analysis of a pectic polysaccharide (Bupleuran 2IIc) with anti-ulcer activity, isolated from the roots of Bupleurum falcatum L., revealed (1----4)-linked alpha-GalA together with small proportions of 2,4- and 3,4-linked GalA, and variously linked neutral sugars. Digestion of Bupleuran 2IIc with endo-alpha-(1----4)-polygalacturonase gave mainly galacturono-oligosaccharides (PG-4) and small proportions of enzyme-resistant regions (PG-1-3). PG-1 contained the sequence----4)GalA- (1----2)-Rha-(1----4)-GalA-(1----, and partial acid hydrolysis gave GalA-(1----4)-Rha, GlcA-(1----4)-Rha, and several di- and oligosaccharides consisting variously of Xyl, Glc, Gal, and Man. PG-2 and PG-3 each contained Rha, Fuc, Ara, Xyl, Man, Gal, Glc, GalA, GlcA, 2-Me-Fuc, 2-Me-Xyl, apiose (Api), aceric acid (AceA), and 3-deoxy-D-manno-2-octulosonic acid (Kdo). PG-4 contained (1----4)-linked alpha-galacturono-di-to-penta- saccharides and GalA. The galacturono-tetra- and -penta-saccharides had one and three methyl-esterified GalA units, respectively, and some of the galacturono-oligosaccharides contained 2,4- or 2,3-linked GalA.

Anti-Ulcer Agents↗

PubMed1994

Characterisation of an anti-ulcer pectic polysaccharide from leaves of Panax ginseng C.A. Meyer.

Structural characterisation of an anti-ulcer polysaccharide (GL-BIII), purified from leaves of Panax ginseng C.A. Meyer, was studied. Methylation analysis indicated that GL-BIII consisted mainly of terminal Arap, 4- or 5-substituted Ara, 2,4-disubstituted Rha, 4- and 6-substituted Gal, and 3,6-disubstituted Gal. Single radial gel diffusion using beta-glucosyl-Yariv antigen indicated that GL-BIII contained a small proportion of a beta-(1-->3,6)-galactan moiety. GL-BIII also contained terminal, 4-substituted, and 3,4-disubstituted GalA, and terminal and 4-substituted GlcA. Base-catalysed beta-elimination suggested that some 2-substituted Rha in GL-BIII was attached to position 4 of a 4-substituted uronic acid. Both mild acid hydrolysis and endo-alpha-(1-->4)-polygalacturonase digestion of GL-BIII did not give fragments consisting mainly of GalA. Methylation analysis and GC-MS analysis of acidic oligosaccharides liberated by partial acid hydrolysis indicated that GL-BIII contained a GalA-(1-->4)-Rha unit in addition to longer acidic units consisting of 2-substituted Rha and 4-substituted GalA. Lithium-mediated degradation of GL-BIII followed by borohydride reduction gave small amounts of fractions containing long and intermediate neutral oligosaccharide-alditols and a large amount of a fraction containing short oligosaccharide-alditols. The long neutral oligosaccharide-alditol fraction mainly comprised 4- or 5-substituted Ara, terminal Galf, 6-substituted Glc, and 2-substituted Man, whereas the intermediate oligosaccharide-alditol fraction consisted mainly of terminal and 6-substituted Galp, 6-substituted Glc, and 2-substituted Man. Methylation analysis and GC-MS analysis of the short oligosaccharide-alditol fraction suggested that it contained at least 14 kinds of di- to tetra-saccharide-alditols such as Gal-(1-->2)-Rha-ol, Gal-(1-->4)-Rha-ol, Ara-->Ara-ol, and Ara-->Ara-->Ara-ol.

Carbohydrate Sequence↗

PubMed1992

Characterization of carbohydrate metabolism and demonstration of glycosomes in a Phytomonas sp. isolated from Euphorbia characias.

Phytomonas sp. isolated from Euphorbia characias was adapted to SDM-79 medium. Cells isolated in the early stationary phase of growth were analyzed for their capacity to utilize plant carbohydrates for their energy requirements. The cellulose-degrading enzymes amylase, amylomaltase, invertase, carboxymethylcellulase, and the pectin-degrading enzymes polygalacturonase and oligo-D-galactosiduronate lyase were present in Phytomonas sp. and were all, except for amylomaltase, excreted into the external medium. Glucose, fructose and mannose served as the major energy substrates. Catabolism of carbohydrates occurred mainly via aerobic glycolysis according to the Embden-Meyerhof pathway, of which all the enzymes were detected. Likewise, the end-products of glycolysis, acetate and pyruvate, glycerol, succinate and ethanol were detected in the culture medium, as were the enzymes responsible for their production. Mitochondria were incapable of oxidizing succinate, 2-oxoglutarate, pyruvate, malate and proline, but had a high capacity to oxidize glycerol 3-phosphate. This oxidation was completely inhibited by salicylhydroxamic acid. No cytochromes could be detected either in intact mitochondria or in sub-mitochondrial particles. Mitochondrial respiration was not inhibited by antimycin, azide or cyanide. The glycolytic enzymes, from hexokinase to phosphoglycerate kinase, and the enzymes glycerol kinase, glycerol-3-phosphate dehydrogenase, phosphoenolpyruvate carboxykinase, malate dehydrogenase and adenylate kinase, were all associated with glycosomes that had a buoyant density of about 1.24 g cm-1 in sucrose. Cytochemical staining revealed the presence of catalase in these organelles. The cytosolic enzyme pyruvate kinase was activated by fructose 2,6-bisphosphate, typical of all other pyruvate kinases from Kinetoplastida. The energy metabolism of the plant parasite Phytomonas sp. isolated from E. characias resembled that of the bloodstream form of the mammalian parasite Trypanosoma brucei.

Animals↗

PubMed1996

Lactic acid fermentation of cassava dough into agbelima.

The souring of cassava dough during fermentation into the fermented cassava meal, agbelima, was investigated. Four different types of traditional inocula were used to ferment the dough and increases in titrable acidity expressed as lactic acid from 0.31-0.38 to 0.78-0.91% (w/w) confirmed the fermentation to be a process of acidification. The microflora of all inocula and fermenting dough contained high counts of lactic acid bacteria, 10(8)-10(9) cfu/g in all inocula and 10(7)-10(8), 10(8)-10(9) and 10(9) cfu/g at 0, 24 and 48 h in all fermentations. Lactobacillus plantarum was the dominant species of lactic acid bacteria during all types of fermentation accounting for 51% of 171 representative isolates taken from various stages of fermentation. Other major lactic acid bacteria found were Lactobacillus brevis, 16%, Leuconostoc mesenteroides, 15% and some cocci including Streptococcus spp. whose numbers decreased with fermentation time. The lactic acid bacteria were responsible for the souring of agbelima through the production of lactic acid. All L. plantarum, L. brevis and L. mesenteroides isolates examined demonstrated linamarase as well as other enzymatic activities but did not possess tissue degrading enzymes like cellulase, pectin esterase and polygalacturonase. The aroma profile of agbelima did not vary with the type of inoculum used and in all samples the build-up of aroma compounds were dominated by a non-identified low molecular weight alcohol, 1-propanol, isoamyl alcohol, ethyl acetate, 3-methyl-1-butanol and acetoin. Substantial reductions occurred in the levels of cyanogenic compounds present in cassava during fermentation into agbelima and detoxification was enhanced by the use of inoculum.

Colony Count, Microbial↗

PubMed1990

An automated spectrophotometric flow-injection procedure for the determination of cellulase activity in bioreactor preparations.

A spectrophotometric procedure for the determination of cellulase activity in precipitated bioreactor preparations and culture filtrates is described. It is based on the determination of reducing sugar produced by the action of the enzyme on carboxymethylcellulose. The reducing sugar is derivatized with p-aminobenzoyl-hydrazide and permits a limit of detection of 0.1 U ml-1 cellulase in the presence of background sugar, with a sampling rate of 5 h-1. The method can readily be applied to the determination of any carbohydrase acting on soluble substrates and producing reducing sugars, e.g. amylase, dextranase, xylanase, glucanase and polygalacturonase.

Calibration↗